X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=8c935992ed529e658cc29d37de942ccc87518a7f;hb=37a5dfc3c72a42689e90ad8a0e118e8855d9868b;hp=b1a8b8bb2cbc279772ba7c5bca5158274fd8c232;hpb=739be60490b5c6efe5237ff12605baa6b38035f4;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index b1a8b8b..8c93599 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -341,30 +341,38 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
 
   public void setScrollValues(int x, int y)
   {
+    int width = av.alignment.getWidth();
+    int height = av.alignment.getHeight();
+
+    if(av.hasHiddenColumns)
+     width = av.getColumnSelection().findColumnPosition(width);
+
     av.setStartRes(x);
     av.setStartSeq(y);
-    av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1);
+
+    av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) -1);
 
     hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
     vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
 
-    if (hextent > av.alignment.getWidth())
+    if (hextent > width)
     {
-      hextent = av.alignment.getWidth();
+      hextent = width;
     }
-    if (vextent > av.alignment.getHeight())
+
+    if (vextent > height)
     {
-      vextent = av.alignment.getHeight();
+      vextent = height;
     }
 
-    if (hextent + x > av.getAlignment().getWidth())
+    if ( (hextent + x) > width)
     {
-      x = av.getAlignment().getWidth() - hextent;
+      x = width - hextent;
     }
 
-    if (vextent + y > av.getAlignment().getHeight())
+    if ( (vextent + y) > height)
     {
-      y = av.getAlignment().getHeight() - vextent;
+      y = height - vextent;
     }
 
     if (y < 0)
@@ -389,6 +397,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
 
     if(overviewPanel!=null)
           overviewPanel.setBoxPosition();
+
   }
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
@@ -477,9 +486,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
 
     if (av.getWrapAlignment())
     {
-      int max = av.alignment.getWidth() /
-          seqPanel.seqCanvas.
-          getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +1;
+      int maxwidth = av.alignment.getWidth();
+
+      if (av.hasHiddenColumns)
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+      int max = maxwidth /
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +
+          1;
+
       vscroll.setMaximum(max);
       vscroll.setUnitIncrement(1);
       vscroll.setVisibleAmount(1);